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. 2016 Sep 15;4(5):e01000-16. doi: 10.1128/genomeA.01000-16

Permanent Draft Genome Sequence of Frankia sp. Strain BR, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equisetifolia

Timothy D’Angelo 1, Rediet Oshone 1, Feseha Abebe-Akele 1, Stephen Simpson 1, Krystalynne Morris 1, W Kelley Thomas 1, Louis S Tisa 1,✉
PMCID: PMC5026450  PMID: 27635010

Abstract

Frankia sp. strain BR is a member of Frankia lineage Ic and is able to reinfect plants of the Casuarinaceae family. Here, we report a 5.2-Mbp draft genome sequence with a G+C content of 70.0% and 4,777 candidate protein-encoding genes.

GENOME ANNOUNCEMENT

Members of the genus Frankia are nitrogen-fixing actinobacteria that form an endophytic symbiosis with actinorhizal plants (1). This group of woody dicotyledonous plants is distributed worldwide and comprises over 200 species from eight angiosperm families (2). Because of its symbiosis with Frankia spp., actinorhizal plants play important ecological roles as pioneer species and are used in agroforestry, land reclamation, crop protection, and soil stabilization projects (3–5). Molecular phylogenetic approaches have identified four major clusters of Frankia (6–9), and genomes for representatives from each cluster have been sequenced (10–28). The availability of these Frankia genome databases has opened up the use of “omics” approaches. Furthermore, analysis of Frankia genomes has revealed new potential in respect to metabolic diversity, natural product biosynthesis, and stress tolerance, which may aid the cosmopolitan nature of the actinorhizal symbiosis.

Actinorhizal plants belonging to the Casuarinaceae family are able to grow under saline conditions and have been used extensively as a green barrier (28–33). Casuarina trees are native to tropical areas of Australia and the South Pacific and have subsequently been transplanted to other tropical areas of the world, particularly Africa (34). In countries such as Egypt, Tunisia, and Senegal, Casuarina trees are actively used in agroforestry and as windbreaks and shelterbelts for agriculture in arid areas (32, 35, 36). Members of Frankia cluster 1c have the most restricted host range and are able to infect only Casuarina and Allocasuarina host plants (1, 18). Frankia sp. strain BR was isolated from axenic Casuarina equisetifolia root nodules that had been inoculated with crushed C. equisetifolia root nodules from Brazil (37). The Frankia sp. strain BR genome was sequenced to provide information on cluster 1c lineage and symbiosis with Casuarina trees.

Sequencing of the draft genome of Frankia sp. strain BR was performed at the Hubbard Center for Genome Studies (University of New Hampshire, Durham, NH, USA) using Illumina technology techniques (38). A standard Illumina shotgun library was constructed and sequenced using the Illumina HiSeq2500 platform, which generated 24,720,192 reads (260-bp insert size) totaling 3,708 Mbp. The Illumina sequence data were assembled using CLC Genomics workbench version 8.5 and ALLPaths-LG version r41043 (39). The final draft assembly for Frankia sp. strain BR consisted of 180 contigs with an N50 contig size of 60.2 kb and 450.4× coverage of the genome. The final assembled genome contained a total sequence length of 5,227,240 bp with a G+C content of 70.0%.

The assembled Frankia sp. strain BR was annotated via the Integrated Microbial Genomes (IMG) platform developed by the Joint Genome Institute, Walnut Creek, CA, USA (40, 41), resulting in 4,777 candidate protein-encoding genes and 46 tRNA and two rRNA regions.

Accession number(s).

This whole-genome shotgun sequence has been deposited at DDBJ/EMBL/GenBank under the accession number LRTJ00000000. The version described in this paper is the first version, LRTJ01000000.

ACKNOWLEDGMENTS

Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2681. This work was supported by USDA National Institute of Food and Agriculture Hatch Project 022821 (L.S.T.), Agriculture and Food Research Initiative Grant 2015-67014-22849 from the USDA National Institute of Food and Agriculture (L.S.T.), and the College of Life Science and Agriculture at the University of New Hampshire–Durham. Sequencing was performed on an Illumina HiSeq2500 purchased with an NSF MRI grant (DBI-1229361) to W.K.T.

Footnotes

Citation D’Angelo T, Oshone R, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequence of Frankia sp. strain BR, a nitrogen-fixing actinobacterium isolated from the root nodules of Casuarina equisetifolia. Genome Announc 4(5):e01000-16. doi:10.1128/genomeA.01000-16.

REFERENCES

  • 1.Normand P, Benson DR, Berry AM, Tisa LS. 2014. Family Frankiaceae, p. 339–356. In Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (ed), The prokaryote—actinobacteria, 4th ed. Springer, Berlin. [Google Scholar]
  • 2.Benson DR, Vandenheuvel B, Potter D. 2004. Actinorhizal symbioses: diversity and biogeography, p. 99–127. In Gillings M, Holmes A (ed), Plant microbiology. BIOS Scientific Publishers, Oxford, UK. [Google Scholar]
  • 3.Dommergues YR. 1997. Contribution of actinorhizal plants to tropical soil productivity and rehabilitation. Soil Biol Biochem 29:931–941. doi: 10.1016/S0038-0717(96)00227-1. [DOI] [Google Scholar]
  • 4.Kohls SJ, Baker DD, Van Kessel C, Dawson JO. 2003. An assessment of soil enrichment by actinorhizal N2 fixation using δ15N values in a chronosequence of deglaciation at Glacier Bay, Alaska. Plant Soil 254:11–17. doi: 10.1023/A:1024950913234. [DOI] [Google Scholar]
  • 5.Benson DR, Dawson JO. 2007. Recent advances in the biogeography and genecology of symbiotic Frankia and its host plants. Physiol Plant 130:318–330. doi: 10.1111/j.1399-3054.2007.00934.x. [DOI] [Google Scholar]
  • 6.Normand P, Orso S, Cournoyer B, Jeannin P, Chapelon C, Dawson J, Evtushenko L, Misra AK. 1996. Molecular phylogeny of the genus Frankia and related genera and emendation of the family Frankiaceae. Int J Syst Bacteriol 46:1–9. doi: 10.1099/00207713-46-1-1. [DOI] [PubMed] [Google Scholar]
  • 7.Cournoyer B, Lavire C. 1999. Analysis of Frankia evolution radiation using glnII sequences. FEMS Microbiol Lett 177:29–34. doi: 10.1111/j.1574-6968.1999.tb13709.x. [DOI] [PubMed] [Google Scholar]
  • 8.Nouioui I, Ghodhbane-Gtari F, Beauchemin NJ, Tisa LS, Gtari M. 2011. Phylogeny of members of the Frankia genus based on gyrB, nifH and glnII sequences. Antonie Van Leeuwenhoek 100:579–587. doi: 10.1007/s10482-011-9613-y. [DOI] [PubMed] [Google Scholar]
  • 9.Ghodhbane-Gtari F, Nouioui I, Chair M, Boudabous A, Gtari M. 2010. 16S–23S rRNA intergenic spacer region variability in the genus Frankia. Microbiol Ecol 60:487–495. doi: 10.1007/s00248-010-9641-6. [DOI] [PubMed] [Google Scholar]
  • 10.Tisa LS, Oshone R, Sarkar I, Ktari A, Sen A, Gtari M. 2016. Genomic approaches toward understanding the actinorhizal symbiosis: an update on the status of the Frankia genomes. Symbiosis [Epub ahead of print.] doi: 10.1007/s13199-016-0390-2. [DOI] [Google Scholar]
  • 11.D’Angelo T, Oshone R, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permanent draft genome sequence for Frankia sp. strain EI5c, a single-spore isolate of a nitrogen-fixing actinobacterium, isolated from the root nodules of Elaeagnus angustifolia. Genome Announc 4(4):e00660-16. doi: 10.1128/genomeA.00660-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Ghodhbane-Gtari F, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, Land ML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, Pati A, Pitluck S, Santos CL, Sen A, Sur S, Szeto E, Tavares F, Teshima H, Thakur S, Wall LG, Woyke T, Tisa LS. 2013. Draft genome sequence of Frankia sp. strain CN3, an atypical, noninfective (nod−) ineffective (fix−) isolate from Coriaria nepalensis. Genome Announc 1(2):00085-13. doi: 10.1128/genomeA.00085-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Ghodhbane-Gtari F, Hurst SG IV, Oshone R, Morris K, Abebe-Akele F, Thomas WK, Ktari A, Salem K, Gtari M, Tisa LS. 2014. Draft genome sequence of Frankia sp. strain BMG5.23, a salt-tolerant nitrogen-fixing actinobacterium isolated from the root nodules of Casuarina glauca grown in Tunisia. Genome Announc 2(3):e00520-14. doi: 10.1128/genomeA.00520-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Gtari M, Ghodhbane-Gtari F, Nouioui I, Ktari A, Hezbri K, Mimouni W, Sbissi I, Ayari A, Yamanaka T, Normand P, Tisa LS, Boudabous A. 2015. Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains. Sci Rep 5:13112. doi: 10.1038/srep13112. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Hurst SG IV, Ghodhbane-Gtari F, Oshone R, Morris K, Abebe-Akele F, Thomas WK, Ktari A, Salem K, Mansour S, Gtari M, Tisa LS. 2014. Draft genome sequence of Frankia sp. strain Thr, a nitrogen-fixing actinobacterium isolated from the root nodules of Casuarina cunninghamiana grown in Egypt. Genome Announc 2(3):e00493-14. doi: 10.1128/genomeA.00493-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Mansour SR, Oshone R, Hurst SG IV, Morris K, Thomas WK, Tisa LS. 2014. Draft genome sequence of Frankia sp. strain CcI6, a salt-tolerant nitrogen-fixing actinobacterium isolated from the root nodule of Casuarina cunninghamiana. Genome Announc 2(1):e01205-13. doi: 10.1128/genomeA.01205-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Ngom M, Oshone R, Hurst SG IV, Abebe-Akele F, Simpson S, Morris K, Sy MO, Champion A, Thomas WK, Tisa LS. 2016. Permanent draft genome sequence for Frankia sp. strain CeD, a nitrogen-fixing actinobacterium isolated from the root nodules of Casuarina equistifolia grown in Senegal. Genome Announc 4(2):e00265-16. doi: 10.1128/genomeA.00265-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Normand P, Lapierre P, Tisa LS, Gogarten JP, Alloisio N, Bagnarol E, Bassi CA, Berry AM, Bickhart DM, Choisne N, Couloux A, Cournoyer B, Cruveiller S, Daubin V, Demange N, Francino MP, Goltsman E, Huang Y, Kopp OR, Labarre L, Lapidus A, Lavire C, Marechal J, Martinez M, Mastronunzio JE, Mullin BC, Niemann J, Pujic P, Rawnsley T, Rouy Z, Schenowitz C, Sellstedt A, Tavares F, Tomkins JP, Vallenet D, Valverde C, Wall LG, Wang Y, Medigue C, Benson DR. 2007. Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17:7–15. doi: 10.1101/gr.5798407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Nouioui I, Beauchemin N, Cantor MN, Chen A, Detter JC, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Hua SX, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nordberg HP, Ovchinnikova G. 2013. Draft genome sequence of Frankia sp. strain BMG5.12, a nitrogen-fixing actinobacterium isolated from Tunisian soils. Genome Announc 1(4):e00468-13. doi: 10.1128/genomeA.00468-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Oshone R, Hurst SG IV, Abebe-Akele F, Simpson S, Morris K, Thomas WK, Tisa LS. 2016. Permeant draft genome sequences for two variants of Frankia sp. strain CpI1, the first Frankia strain isolated from the root nodule of Comptonia peregrina. Genome Announc 4(1):e01588-15. doi: 10.1128/genomeA.01588-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Persson T, Benson DR, Normand P, Vanden Heuvel B, Pujic P, Chertkov O, Teshima H, Bruce DC, Detter C, Tapia R, Han S, Han J, Woyke T, Pitluck S, Pennacchio L, Nolan M, Ivanova N, Pati A, Land ML, Pawlowski K, Berry AM. 2011. Genome sequence of “Candidatus Frankia datiscae” Dg1, the uncultured microsymbiont from nitrogen-fixing root nodules of the dicot Datisca glomerata. J Bacteriol 193:7017–7018. doi: 10.1128/JB.06208-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Pujic P, Bolotin A, Fournier P, Sorokin A, Lapidus A, Richau KH, Briolay J, Mebarki F, Normand P, Sellstedt A. 2105. Genome sequence of the atypical symbiotic Frankia R43 strain, a nitrogen-fixing and hydrogen-evolving actinobacterium. Genome Announc 3(6):e01387-15. doi: 10.1128/genomeA.01387-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Sen A, Beauchemin N, Bruce D, Chain P, Chen A, Walston Davenport K, Deshpande S, Detter C, Furnholm T, Ghodbhane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Ivanova N, Kyrpides N, Land ML, Markowitz V, Mavrommatis K, Nolan M, Nouioui I, Pagani I, Pati A, Pitluck S, Santos CL, Sur S, Szeto E, Tavares F, Teshima H, Thakur S, Wall L, Wishart J, Woyke T, Tisa LS. 2013. Draft genome sequence of Frankia sp. strain QA3, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus nitida. Genome Announc 1(2):e00103-13. doi: 10.1128/genomeA.00103-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permanent draft genome sequence of Frankia sp. strain ACN1ag, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus glutinosa. Genome Announc 3(6):e01483-15. doi: 10.1128/genomeA.01483-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Swanson E, Oshone R, Simpson S, Morris K, Abebe-Akele F, Thomas WK, Tisa LS. 2015. Permeant draft genome sequence of Frankia sp. strain AvcI1, a nitrogen-fixing actinobacterium isolated from the root nodule of Alnus viridis subsp. crispa grown in Canada. Genome Announc 3(6):e01511-15. doi: 10.1128/genomeA.01511-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Tisa LS, Beauchemin N, Gtari M, Sen A, Wall LG. 2013. What stories can the Frankia genomes start to tell us? J Biosci 38:719–726. doi: 10.1007/s12038-013-9364-1. [DOI] [PubMed] [Google Scholar]
  • 27.Tisa LS, Beauchemin N, Cantor MN, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Copeland A, Gtari M, Huntemann M, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nouioui I, Oshone R, Ovchinnikova G, Pagani I, Palaniappan K, Pati A. 2015. Draft genome sequence of Frankia sp. strain DC12, an atypical, noninfective, ineffective isolate from Datisca cannabina. Genome Announc 3(4):e00889-15. doi: 10.1128/genomeA.00889-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 28.Wall LG, Beauchemin N, Cantor MN, Chaia E, Chen A, Detter JC, Furnholm T, Ghodhbane-Gtari F, Goodwin L, Gtari M, Han C, Han J, Huntemann M, Hua SX, Ivanova N, Kyrpides N, Markowitz V, Mavrommatis K, Mikhailova N, Nordberg HP, Nouioui I, Ovchinnikova G, Pagani I, Pati A, Sen A, Sur S, Szeto E, Thakur S, Wei C-L, Woyke T, Tisa LS. 2013. Draft genome sequence of Frankia sp. strain BCU110501, a nitrogen-fixing actinobacterium isolated from nodules of Discaria trinevis. Genome Announc 1(4):e00503-13. doi: 10.1128/genomeA.00503-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.El-Lakany MH, Luard EJ. 1983. Comparative salt tolerance of selected Casuarina species. Aust Forest Res 13:11–20. [Google Scholar]
  • 30.Girgis MGZ, Ishac YZ, Diem HG, Dommergues YR. 1992. Selection of salt tolerant Casuarina glauca and Frankia. Acta Oecol 13:443–451. [Google Scholar]
  • 31.Mailly D, Ndiaye P, Margolis HA, Pineau M. 1994. Fixation des dunes et reboisement avec le filao (Casuarina equisetifolia) dans la zone du littoral nord du Senegal. Forest Chron 70:282–290. doi: 10.5558/tfc70282-3. [DOI] [Google Scholar]
  • 32.El-Lakany MH. 1983. A review of breeding drought resistant Casuarina for shelterbelt establishment in arid regions with special reference to Egypt. Forest Ecol Manage 6:129–137. doi: 10.1016/0378-1127(83)90017-8. [DOI] [Google Scholar]
  • 33.Tani C, Sasakawa H. 2003. Salt tolerance of Casuarina equisetifolia and Frankia Ceq1 strain isolated from the root nodules of C. equisetifolia. Soil Sci Plant Nutr 49:215–222. doi: 10.1080/00380768.2003.10410000. [DOI] [Google Scholar]
  • 34.Gtari M, Dawson JO. 2011. An overview of actinorhizal plants in Africa. Funct Plant Biol 38:653–661. doi: 10.1071/FP11009. [DOI] [PubMed] [Google Scholar]
  • 35.Mailly D, Margolis HA. 1992. Forest floor and mineral soil development in Casuarina equisetifolia plantations on the coastal sand dunes of Senegal. Forest Ecol Manag 55:259–278. doi: 10.1016/0378-1127(92)90105-I. [DOI] [Google Scholar]
  • 36.Zhong C, Mansour S, Nambiar-Veetil M, Bogusz D, Franche C. 2013. Casuarina glauca: a model tree for basic research in actinorhizal symbiosis. J Biosci 38:815–823. doi: 10.1007/s12038-013-9370-3. [DOI] [PubMed] [Google Scholar]
  • 37.Müller A, Benoist P, Diem HG, Schwencke J. 1991. Age-dependent changes in extracellular proteins, aminopeptidase and proteinase activities in Frankia isolate BR. J Gen Microbiol 137:2787–2796. doi: 10.1099/00221287-137-12-2787. [DOI] [PubMed] [Google Scholar]
  • 38.Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433–438. doi: 10.1517/14622416.5.4.433. [DOI] [PubMed] [Google Scholar]
  • 39.Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513–1518. doi: 10.1073/pnas.1017351108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res 34:D344–D348. doi: 10.1093/nar/gkj024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. 2009. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25:2271–2278. doi: 10.1093/bioinformatics/btp393. [DOI] [PubMed] [Google Scholar]

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